Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 28.85 kDa 
• Atom Count: 1912 
• Modelled Residue Count: 231 
• Deposited Residue Count: 249 
• Unique protein chains: 2

1RE1

CRYSTAL STRUCTURE OF CASPASE-3 WITH A NICOTINIC ACID ALDEHYDE INHIBITOR

• DOI: 10.2210/pdb1RE1/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-11-06 Released: 2004-05-11 
• Deposition Author(s): Becker, J.W., Rotonda, J., Soisson, S.M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.261 
• R-Value Work: 0.194 

Literature

Reducing the Peptidyl Features of Caspase-3 Inhibitors: A Structural Analysis

Becker, J.W., Rotonda, J., Soisson, S.M., Aspiotis, R., Bayly, C., Francoeur, S., Gallant, M., Garcia-Calvo, M., Giroux, A., Grimm, E., Han, Y., Mckay, D., Nicholson, D.W., Peterson, E., Renaud, J., Roy, S., Thornberry, N., Zamboni, R.

(2004) J Med Chem 47: 2466-2474

• PubMed: 15115390 
• DOI: 10.1021/jm0305523
• Primary Citation of Related Structures:  
  1RE1, 1RHM, 1RHK, 1RHJ, 1RHU, 1RHR, 1RHQ


• PubMed Abstract: 
  

Caspases are cysteine proteases that specifically cleave Asp-Xxx bonds. They are key agents in inflammation and apoptosis and are attractive targets for therapy against inflammation, neurodegeneration, ischemia, and cancer. Many caspase structures are known, but most involve either peptide or protein inhibitors, unattractive candidates for drug development. We present seven crystal structures of inhibited caspase-3 that illustrate several approaches to reducing the peptidyl characteristics of the inhibitors while maintaining their potency and selectivity. The inhibitors reduce the peptidyl nature of inhibitors while preserving binding potency by (1). exploiting a hydrophobic binding site C-terminal to the cleavage site, (2). replacing the negatively charged aspartyl residue at P4 with neutral groups, and (3). using a peptidomimetic 5,6,7-tricyclic system or a pyrazinone at P2-P3. In addition, we have found that two nicotinic acid aldehydes induce a significant conformational change in the S2 and S3 subsites of caspase-3, revealing an unexpected binding mode. These results advance the search for caspase-directed drugs by revealing how unacceptable molecular features can be removed without loss of potency.

---

Organizational Affiliation: 

Departments of Medicinal Chemistry and Metabolic Disorders, Merck Research Laboratory, PO Box 2000, Rahway, New Jersey 07065, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-3	A	147	Homo sapiens	Mutation(s): 0  Gene Names: CASP3, CPP32 EC: 3.4.22 (PDB Primary Data), 3.4.22.56 (UniProt)
Find proteins for P42574 (Homo sapiens) Explore P42574  Go to UniProtKB:  P42574
NIH Common Fund Data Resources
PHAROS:  P42574 GTEx:  ENSG00000164305

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-3	B	102	Homo sapiens	Mutation(s): 0  Gene Names: CASP3, CPP32 EC: 3.4.22 (PDB Primary Data), 3.4.22.56 (UniProt)
Find proteins for P42574 (Homo sapiens) Explore P42574  Go to UniProtKB:  P42574
NIH Common Fund Data Resources
PHAROS:  P42574 GTEx:  ENSG00000164305

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA3	A	(3S)-3-{[(5-BROMOPYRIDIN-3-YL)CARBONYL]AMINO}-4-OXOBUTANOIC ACID C10 H9 Br N2 O4 FBMPVEGAIMRCBG-QMMMGPOBSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
NA3	IC50 :  6117   nM  PDBBind
NA3	IC50:  6000   nM  BindingDB
NA3	IC50:  6117   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.261 
• R-Value Work: 0.194 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.78	α = 90
b = 83.76	β = 90
c = 95.91	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
SAINT	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-11-06 
• Released Date: 2004-05-11 
Deposition Author(s): Becker, J.W., Rotonda, J., Soisson, S.M.

Revision History  

• Version 1.0: 2004-05-11
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance